The 2003 series was good, but never excited me as much because (a) I didn't watch it when it was new, and (b) In many ways it was a watered down version of Mirage and wasn't quite as impressive. I kept seeing all the little ways it was toned down for children.
And as gay men, my friends and I noticed things we could relate most to. A lifetime of personal experiences, conventional wisdom and cold-reading develops an intuition often called "gaydar." And believe me, there's a huge difference between love of one's own brothers, and romantic attachment between men. But also, for most gay men, only a tiny part of being gay is directly relevant to sexuality, and there are other quirks at play too. Raph's other mannerisms all accumulated to strongly suggest that, like most gay men, he identifies as male but has a brain wired more like that of a woman, which affects aspects of his emotional responses, instinct, intuitions and overall personality, which are shared by most hetero women including very tomboyish women. (A separate psychological correlation has been observed between a majority of lesbians and hetero men.) The fact that Raph's personality was always a lot more like April or Karai than like Leo, Mikey or Donnie was not subtle at all. All in all, Raphael kept ringing all the right alarm bells in our brains. But these personality traits conspicuously started to fade away during season 3, and it was like, "what the hell, Nick?"
Earlier, I had this discussion with Yoshimickster, who isn't gay, but agrees that the signals being perceived by gay audiences were really being seen by them—none of us imagined what we were seeing. But he illustrated how, on a TV show, it's a lot more complicated than that. TMNT has a whole production team of lots of writers, etc. When a show makes a decision to change something, they'll usually find a way to make it happen, no matter how many inconsistencies it may create.
But since those early signals were real, it's all the more infuriating that the show ended up doing what it did. Gay audiences don't necessarily ask for smut or anything like that. But there are plenty of gay people with self-respect as a demographic, and they want to feel visible and relevant and respected in mainstream culture, no matter the age of the target audience. Gay people are already used to feeling invisible on TV when children are expected to be watching. But to be made to feel visible, and then invisible, is not easily excused. It's genuinely offensive, and sends exactly the wrong message to vulnerable gay youth. It's straightwashing.